4 Answers
4

The mystery is Christ and our mystical union to him. Hodge pretty much answers the question as simply as possible:

Τὸ μυστήριον τοῦτο μεγα ἐστίν, this mystery is great. The word mystery does not refer to the passage in Gen. 2:24, as though the apostle intended to say that that passage had a mystical sense which he had just unfolded by applying it to the relation between Christ and his church. It is the union between Christ and his people, the fact that they are one flesh, he declares to be a great mystery. (Charles Hodge, Ephesians p350)

He himself is a great and unfathomable mystery:

Beyond all question, the mystery from which true godliness springs is great:
He appeared in the flesh,
was vindicated by the Spirit,
was seen by angels,
was preached among the nations,
was believed on in the world,
was taken up in glory. (ESV, 1 Timothy 3:16)

To add to this mystery of Christ that somehow every believer is united into a single body in his flesh, is indeed a very great mystery that no man can either fully know or explain. That believers are literally in some mystical sense united to the person of Christ and thus died and risen in him to new life is central to Pauline theology (Col 2:6-15, Eph 3).

This 'mystery' or Christ, or the gospel, as Paul elsewhere refers to from various angles is to be taken as 'a long held divine secret only' now at last disclosed. Therefore even though this mystery is not referring to marriage directly yet that primary institution of human society is now seen as formerly declared in shadowy words at the beginning compared to our understanding in the gospel now. Under Pauline usage, nothing can be understood until the 'mystery of Christ' is put in the centre of our view. It is from this 'great mystery' and our mystical union to him, that Paul resolves all wisdom, meaning and explanation of all truth.

Paul has referred to the conjunctions within the Pleroma ... when writing of the conjugal union ... thus: "This is a great mystery, but I speak concerning Christ and the Church."(Irenaeus, Against Heresies, I-117, ca. 175-225 CE)

το μυστηριον τουτο μεγα εστιν (TR & GMT)

Eph. 5:32 reads as if Paul might be revealing one of the secretive Masonic mysteries. But, he simply compared marriage to the union of Christ and the church. He makes that plain by the next words: εγω δε λεγω εις χριστον και εις την εκκλησιαν:

"Not calling your attention to the mere human relationship, but to the mysterious relation between Christ and His Church,..." (Vincent, Word Studies).

I do agree with this interpretation of the passage. I just wonder about Paul's wording in this passage. He was very selective of his wording in past scriptures and it seems to me "profound mystery" dignifies a more complex interpretation than face value.
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KrisSep 14 '13 at 22:48

Looking only at verse 32, it is pretty clear that the profound mystery involves Christ and his relationship with the church. However, looking at the broader passage (probably around 5:21-33) demonstrates that Paul is talking about more. This portion of Ephesians is one of the key passages on marriage relationships, and it is here that Paul explains the marriage relationship as a symbol of the relationship Christ has with his church (compare Revelation 21:9 One of the seven angels who had the seven bowls full of the seven last plagues came and said to me, “Come, I will show you the bride, the wife of the Lamb.”, among other passages).

To summarize the passage, Paul instructs wives to submit to their husbands as to the Lord (as all Christians submit to the Lord). He then instructs husbands to love their wives as Christ loved the church, by giving his life for her. And this is where we find 5:32.

...28 In this same way, husbands ought to love their wives as their own bodies. He who loves his wife loves himself. 29 After all, no one ever hated their own body, but they feed and care for their body, just as Christ does the church— 30 for we are members of his body. 31 “For this reason a man will leave his father and mother and be united to his wife, and the two will become one flesh.” 32 This is a profound mystery—but I am talking about Christ and the church.

It is a profound mystery that a man and woman can be members of each other's bodies. It is a profound mystery that two individuals can become one flesh. In mathematical terms it is like saying 1+1=1, which challenges everything we know and understand. Furthermore, there seems to be a supernatural bond between spouses; this passage tells why. The profound mystery of becoming one flesh and giving up our individual freedom and being supernaturally bound with our spouse highlights the profound mystery of becoming one with Christ and being supernaturally bound to him.

A quick note on the term mystery as used by Paul: it is something that was hidden but is now revealed in Christ.

"Thus he composed a more spiritual Gospel for the use of those who were being perfected. Nevertheless, he yet did not divulge the things not to be uttered, nor did he write down the hierophantic teaching of the Lord, but to the stories already written he added yet others and, moreover, brought in certain sayings of which he knew the interpretation would, as a mystagogue, lead the hearers into the innermost sanctuary of that truth hidden by seven veils."

One might find in the Letter of Clement of Alexandria on Secret Mark (earlychristianwritings.com as one source) further explication of points of contention surrounding the question of expansion of the notion of "one flesh" as extended to the entirety of the Church. I realize this isn't precisely an answer, but the true answer appears to be ineffable (incommunicable by words) by divine design!

Sir - thank you for your time to write this post, but I cannot use this post to teach anyone anything because there are no sources cited nor even some link of thought using verses. You have given us your opinion, which, on this site, does not count as something substantive. In a word, your input is welcome, but is pure anecdote.
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JosephJun 22 '14 at 17:50

To clarify, the quote is from Clement of Alexandria. It may be helpful to review his historical position and status in Christianity, say, here: en.wikipedia.org/wiki/Clement_of_Alexandria ... As for linking verses, I should also note that the quote is extracanonical, and would therefore require one to lend at least provisional weight to such documents. In terms of the canonicals, well, Song of Solomon should be a useful starting point. Isaiah 4:1 as well. Then, I suggest looking for an integration point with NT ethos, and then waiting for direct divine completion of understanding.
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empiricJun 24 '14 at 15:29

Thank you for the clarification. If you have the background, please cite the sources: the closer the sources to the Biblical text, the better. Also, your readers may not have the breadth of knowledge that you have, so feel free to expound your thoughts. THANKS!
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JosephJun 24 '14 at 15:41